I am having a huge amount of difficulty in an issue which seems as though it should be quite simple, due to the way the KEGG data seems to be available and my inability to grasp their short documentation. I have looked through github and available scripts for KEGG although none seem to cover my usage. I am comfortable scripting in Perl, and R, but have used PHP and Curl to access REST APIs in the past with no trouble.

I would essentially like to download a large list in text format of all of the reactions in the human metabolic pathway, which are displayed beautifully in maps on the KEGG website.

Ideally the format would be as follows:

Compound

Product

Metabolism

Enzyme

x

y

fatty acid degradation

lipase

y

z

fatty acid degradation

lipase

I seem to be making no headway and wondered if anybody had obtained anything similar before from the API or the .KPMG or .XML downloads which seem to be available. If anybody could give me an example I can extend this I believe to cover everything.

I have now worked out my problem, which came down to not properly understanding the response data. Essentially everything was returned in KMGL markup. Once you understand the architecture you can extract all the information.